Benchmarking materials property prediction methods: the Matbench test set and Automatminer reference algorithm
Source abstract
Abstract
Abstract We present a benchmark test suite and an automated machine learning procedure for evaluating supervised machine learning (ML) models for predicting properties of inorganic bulk materials. The test suite, Matbench, is a set of 13 ML tasks that range in size from 312 to 132k samples and contain data from 10 density functional theory-derived and experimental sources. Tasks include predicting optical, thermal, electronic, thermodynamic, tensile, and elastic properties given a material’s composition and/or crystal structure. The reference algorithm, Automatminer, is a highly-extensible, fully automated ML pipeline for predicting materials properties from materials primitives (such as composition and crystal structure) without user intervention or hyperparameter tuning. We test Automatminer on the Matbench test suite and compare its predictive power with state-of-the-art crystal graph neural networks and a traditional descriptor-based Random Forest model. We find Automatminer achieves the best performance on 8 of 13 tasks in the benchmark. We also show our test suite is capable of exposing predictive advantages of each algorithm—namely, that crystal graph methods appear to outperform traditional machine learning methods given ~104or greater data points. We encourage evaluating materials ML algorithms on the Matbench benchmark and comparing them against the latest version of Automatminer.
Source: crossref · Quality: baseline
Research context
OpenAlex topics: Machine Learning in Materials Science · X-ray Diffraction in Crystallography · Material Selection and Properties
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
References (53)
Show source-provided references
1. Kohn, W. & Sham, L. J. Self-consistent equations including exchange and correlation effects. Phys. Rev. 140, A1133–A1138 (1965).10.1103/PhysRev.140.A1133 ↗
2. Hohenberg, P. & Kohn, W. Inhomogeneous electron gas. Phys. Rev. 136, B864–B871 (1964).10.1103/PhysRev.136.B864 ↗
3. Mansouri Tehrani, A. et al. Machine learning directed search for ultraincompressible, superhard materials. J. Am. Chem. Soc. 140, 9844–9853 (2018).10.1021/jacs.8b02717 ↗
4. Cooper, C. B. et al. Design-to-device approach affords panchromatic co-sensitized solar cells. Adv. Energy Mater. 9, 1802820 (2019).10.1002/aenm.201802820 ↗
5. Jose, R. & Ramakrishna, S. Materials 4.0: materials big data enabled materials discovery. Appl. Mater. Today 10, 127–132 (2018).10.1016/j.apmt.2017.12.015 ↗
6. Agrawal, A. & Choudhary, A. Perspective: materials informatics and big data: realization of the “fourth paradigm” of science in materials science. APL Mater. 4, 053208 (2016).10.1063/1.4946894 ↗
7. Deng, J. et al. ImageNet: A large-scale hierarchical image database. In 2009 IEEE Conference on Computer Vision and Pattern Recognition 248–255 (IEEE, 2009).10.1109/CVPR.2009.5206848 ↗
8. Rajpurkar, P., Zhang, J., Lopyrev, K. & Liang, P. SQuAD: 100,000+ Questions for Machine Comprehension of Text. Preprint at https://arxiv.org/abs/1606.05250 (2016).10.18653/v1/D16-1264 ↗
9. Castelli, I. E. et al. New cubic perovskites for one- and two-photon water splitting using the computational materials repository. Energy Environ. Sci. 5, 9034 (2012).10.1039/c2ee22341d ↗
10. Hastie, T., Tibshirani, R. & Friedman, J. H. (eds) in The elements of statistical learning: data mining, inference, and prediction 2nd edn., Chapter 7, pp. 241–249 (Springer, 2009).
11. Cawley, G. C. & Talbot, N. L. C. On over-fitting in model selection and subsequent selection bias in performance evaluation. J. Mach. Learn. Res. 11, 2079–2107 (2010).
12. Heckman, J. J. Sample selection bias as a specification error. Econometrica 47, 153 (1979).10.2307/1912352 ↗
13. Alexander J. Smola, Arthur Gretton, Karsten M. Borgwardt & Bernhard Scholkopf. Correcting sample selection bias by unlabeled data. In NIPS’06 Proc. 19th International Conference on Neural Information Processing Systems 601–608 (2006).10.7551/mitpress/7503.003.0080 ↗
14. Miroslav Dud ́ık, Robert E. Schapire & Steven J. Phillips. Correcting sample selection bias in maximum entropy density estimation. In NIPS’05 Proc. 18th International Conference on Neural Information Processing Systems 323–330 (2005).
15. Liu, Y., Zhao, T., Ju, W. & Shi, S. Materials discovery and design using machine learning. J. Materiomics 3, 159–177 (2017).10.1016/j.jmat.2017.08.002 ↗
16. Schmidt, J., Marques, M. R. G., Botti, S. & Marques, M. A. L. Recent advances and applications of machine learning in solid-state materials science. Npj Comput. Mater. 5, 83 (2019).10.1038/s41524-019-0221-0 ↗
17. Wu, Z. et al. MoleculeNet: a benchmark for molecular machine learning. Chem. Sci. 9, 513–530 (2018).10.1039/C7SC02664A ↗
18. Stone, M. Cross-validatory choice and assessment of statistical predictions. J. R. Stat. Soc. Ser. B Methodol. 36, 111–147 (1974).10.1111/j.2517-6161.1974.tb00994.x ↗
19. Ward, L. et al. Matminer: an open source toolkit for materials data mining. Comput. Mater. Sci. 152, 60–69 (2018).10.1016/j.commatsci.2018.05.018 ↗
20. Kabiraj, A., Kumar, M. & Mahapatra, S. High-throughput discovery of high Curie point two-dimensional ferromagnetic materials. Npj Comput. Mater. 6, 35 (2020).10.1038/s41524-020-0300-2 ↗
21. Perdew, J. P. & Yue, W. Accurate and simple density functional for the electronic exchange energy: Generalized gradient approximation. Phys. Rev. B 33, 8800–8802 (1986).10.1103/PhysRevB.33.8800 ↗
22. Clement, C. L., Kauwe, S. K. & Sparks, T. D. Benchmark AFLOW data sets for machine learning. Integr. Mater. Manuf. Innov. 9, 153–156 (2020).10.1007/s40192-020-00174-4 ↗
23. Freedman, D., Pisani, R. & Purves, R. Statistics (international student edition) 4th edn. (W. W. Norton & Company, 2007).
24. Hotelling, H. Analysis of a complex of statistical variables into principal components. J. Edu. Psychol. 24, 417–441 (1933).10.1037/h0071325 ↗
25. Olson, R. S. et al. In Applications of Evolutionary Computation (eds Squillero, G. & Burelli, P.) vol. 9597 pp. 123–137 (Springer International Publishing, 2016).
26. Xie, T. & Grossman, J. C. Crystal graph convolutional neural networks for an accurate and interpretable prediction of material properties. Phys. Rev. Lett. 120, 145301 (2018).10.1103/PhysRevLett.120.145301 ↗
27. Breiman, L. Random forests. Mach. Learn 45, 5–32 (2001).10.1023/A:1010933404324 ↗
28. Ward, L., Agrawal, A., Choudhary, A. & Wolverton, C. A general-purpose machine learning framework for predicting properties of inorganic materials. Npj Comput. Mater. 2, 16028 (2016).10.1038/npjcompumats.2016.28 ↗
29. Faber, F., Lindmaa, A., von Lilienfeld, O. A. & Armiento, R. Crystal structure representations for machine learning models of formation energies. Int. J. Quantum Chem. 115, 1094–1101 (2015).10.1002/qua.24917 ↗
30. Chen, C., Ye, W., Zuo, Y., Zheng, C. & Ong, S. P. Graph networks as a universal machine learning framework for molecules and crystals. Chem. Mater. 31, 3564–3572 (2019).10.1021/acs.chemmater.9b01294 ↗
31. Zhang, Y. & Ling, C. A strategy to apply machine learning to small datasets in materials science. Npj Comput. Mater. 4, 25 (2018).10.1038/s41524-018-0081-z ↗
32. Goodall, R. E. A. & Lee, A. A. Predicting materials properties without crystal structure: Deep representation learning from stoichiometry. Preprint at https://arxiv.org/abs/1910.00617 (2019).
33. Ren, F. et al. Accelerated discovery of metallic glasses through iteration of machine learning and high-throughput experiments. Sci. Adv. 4, eaaq1566 (2018).
34. Meredig, B. et al. Can machine learning identify the next high-temperature superconductor? Examining extrapolation performance for materials discovery. Mol. Syst. Des. Eng. 3, 819–825 (2018).10.1039/C8ME00012C ↗
35. Xiong, Z. et al. Evaluating explorative prediction power of machine learning algorithms for materials discovery using k-fold forward cross-validation. Comput. Mater. Sci. 171, 109203 (2020).10.1016/j.commatsci.2019.109203 ↗
36. Emery, A. A. & Wolverton, C. High-throughput DFT calculations of formation energy, stability and oxygen vacancy formation energy of ABO3 perovskites. Sci. Data 4, 170153 (2017).10.1038/sdata.2017.153 ↗
37. Stein, H. S., Soedarmadji, E., Newhouse, P. F., Guevarra, Dan & Gregoire, J. M. Synthesis, optical imaging, and absorption spectroscopy data for 179072 metal oxides. Sci. Data 6, 9 (2019).10.1038/s41597-019-0019-4 ↗
38. Pedregosa, F. et al. Scikit-learn: machine learning in python. J. Mach. Learn. Res. 12, 2825–2830 (2011).
39. Bernau, C., Augustin, T. & Boulesteix, A.-L. Correcting the optimal resampling-based error rate by estimating the error rate of wrapper algorithms: estimating the error rate of wrapper algorithms. Biometrics 69, 693–702 (2013).10.1111/biom.12041 ↗
40. Krstajic, D., Buturovic, L. J., Leahy, D. E. & Thomas, S. Cross-validation pitfalls when selecting and assessing regression and classification models. J. Cheminforma. 6, 10 (2014).10.1186/1758-2946-6-10 ↗
41. Breiman, L., Friedman, J. H., Olshen, R. A. & Stone, C. J. In Classification And Regression Trees 1st edn. (eds Kimmel J. & Cava, A.) Ch. 5 (Chapman & Hall/CRC, 1984).
42. Jain, A. et al. FireWorks: a dynamic workflow system designed for high-throughput applications: FireWorks: a dynamic workflow system designed for high-throughput applications. Concurr. Comput. Pract. Exp. 27, 5037–5059 (2015).10.1002/cpe.3505 ↗
43. Jain, A. et al. Commentary: The Materials Project: a materials genome approach to accelerating materials innovation. APL Mater. 1, 011002 (2013).10.1063/1.4812323 ↗
44. Ong, S. P. et al. The Materials Application Programming Interface (API): a simple, flexible and efficient API for materials data based on REpresentational State Transfer (REST) principles. Comput. Mater. Sci. 97, 209–215 (2015).10.1016/j.commatsci.2014.10.037 ↗
45. de Jong, M. et al. Charting the complete elastic properties of inorganic crystalline compounds. Sci. Data 2, 150009 (2015).
46. Zhuo, Y., Mansouri Tehrani, A. & Brgoch, J. Predicting the band gaps of inorganic solids by machine learning. J. Phys. Chem. Lett. 9, 1668–1673 (2018).10.1021/acs.jpclett.8b00124 ↗
47. Kawazoe, Y., Yu, J.-Z., Tsai, A.-P. & Masumoto, T. Nonequilibrium Phase Diagrams of Ternary Amorphous Alloys (Springer, 1997).10.1007/b58222 ↗
48. Petousis, I. et al. High-throughput screening of inorganic compounds for the discovery of novel dielectric and optical materials. Sci. Data 4, 160134 (2017).10.1038/sdata.2016.134 ↗
49. Petretto, G. et al. High-throughput density-functional perturbation theory phonons for inorganic materials. Sci. Data 5, 180065 (2018).10.1038/sdata.2018.65 ↗
50. Choudhary, K., Kalish, I., Beams, R. & Tavazza, F. High-throughput identification and characterization of two-dimensional materials using density functional theory. Sci. Rep. 7, 5179 (2017).
51. Conduit, G. & Bajaj, S. Mechanical properties of some steels. https://citrination.com/datasets/153092/ (2017).
52. Kiselyova, N. N., Dudarev, V. A. & Korzhuyev, M. A. Database on the bandgap of inorganic substances and materials. Inorg. Mater. Appl. Res. 7, 34–39 (2016).10.1134/S2075113316010093 ↗
53. Choudhary, K., DeCost, B. & Tavazza, F. Machine learning with force-field-inspired descriptors for materials: fast screening and mapping energy landscape. Phys. Rev. Mater. 2, 083801 (2018).10.1103/PhysRevMaterials.2.083801 ↗